LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
  using 1 OpenMP thread(s) per MPI task
# Initialization
units           metal
boundary        p p p
atom_style      atomic
processors      * * 1     # domain decomposition over x and y

# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data       data.bilayer-graphene # read lammps data file
  orthogonal box = (0 0 -20) to (17.04 19.6761 40)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  256 atoms
  read_data CPU = 0.0488505 secs
mass            1 12.0107   # carbon mass (g/mole) | membrane
mass            2 12.0107   # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor        2.0 bin
neigh_modify    every 1
neigh_modify    delay 0
neigh_modify    check yes
# Separate atom groups
group membrane  type 1
128 atoms in group membrane
group adsorbant type 2
128 atoms in group adsorbant

######################## Potential defition ########################
pair_style  hybrid/overlay  rebo  kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * rebo                 CH.rebo  C C  # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff 1 2 kolmogorov/crespi/z  CC.KC      C C  # long-range
####################################################################

#### Simulation settings ####
timestep  0.0001
velocity  all create 300.0 12345
fix       thermostat all nve
compute   COM1 membrane  com
compute   COM2 adsorbant com
############################

# Output
#dump            1 all xyz 100 trajec.xyz
#dump_modify     1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo          10
thermo_style    custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify   line one format float %14.8f

###### Run molecular dynamics ######
run 1000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 16
  ghost atom cutoff = 16
  binsize = 8, bins = 3 3 8
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair rebo, perpetual
      attributes: full, newton on, ghost
      pair build: full/bin/ghost
      stencil: full/ghost/bin/3d
      bin: standard
  (2) pair kolmogorov/crespi/z, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] 
       0     0.00000000 -1888.67041233 -1898.55881343   300.00000000     0.00000000     3.30000000 
      10     0.00100000 -1888.67037240 -1898.21029916   289.42778520    -0.00020126     3.30020126 
      20     0.00200000 -1888.67021561 -1897.22943631   259.67456089    -0.00041357     3.30041357 
      30     0.00300000 -1888.66999327 -1895.86681330   218.34126559    -0.00063673     3.30063673 
      40     0.00400000 -1888.66978373 -1894.47163849   176.02000692    -0.00087055     3.30087055 
      50     0.00500000 -1888.66966087 -1893.37123396   142.63902861    -0.00111486     3.30111486 
      60     0.00600000 -1888.66966151 -1892.75822768   124.04127204    -0.00136952     3.30136952 
      70     0.00700000 -1888.66976993 -1892.63445770   120.28297806    -0.00163441     3.30163441 
      80     0.00800000 -1888.66992887 -1892.83467481   126.35245790    -0.00190946     3.30190946 
      90     0.00900000 -1888.67006887 -1893.11387088   134.81862143    -0.00219458     3.30219458 
     100     0.01000000 -1888.67013641 -1893.25481870   139.09272852    -0.00248973     3.30248973 
     110     0.01100000 -1888.67011221 -1893.15155809   135.96068294    -0.00279489     3.30279489 
     120     0.01200000 -1888.67001516 -1892.84002980   126.51230266    -0.00311004     3.30311004 
     130     0.01300000 -1888.66989017 -1892.47004258   115.29120969    -0.00343519     3.30343519 
     140     0.01400000 -1888.66979250 -1892.23503136   108.16426724    -0.00377038     3.30377038 
     150     0.01500000 -1888.66976498 -1892.28630603   109.72070258    -0.00411562     3.30411562 
     160     0.01600000 -1888.66982073 -1892.66640631   121.25071190    -0.00447099     3.30447099 
     170     0.01700000 -1888.66993810 -1893.28862656   140.12442720    -0.00483654     3.30483654 
     180     0.01800000 -1888.67007037 -1893.97029277   160.80119589    -0.00521235     3.30521235 
     190     0.01900000 -1888.67016732 -1894.50458806   177.00801243    -0.00559851     3.30559851 
     200     0.02000000 -1888.67019479 -1894.73890125   184.11590729    -0.00599512     3.30599512 
     210     0.02100000 -1888.67014440 -1894.62906034   180.78501933    -0.00640230     3.30640230 
     220     0.02200000 -1888.67003699 -1894.25249122   169.36370739    -0.00682016     3.30682016 
     230     0.02300000 -1888.66991405 -1893.77601632   154.91186768    -0.00724883     3.30724883 
     240     0.02400000 -1888.66982545 -1893.38995103   143.20188490    -0.00768845     3.30768845 
     250     0.02500000 -1888.66980650 -1893.23138955   138.39193054    -0.00813913     3.30813913 
     260     0.02600000 -1888.66986149 -1893.32993943   141.38012473    -0.00860097     3.30860097 
     270     0.02700000 -1888.66996324 -1893.60070625   149.59171759    -0.00907408     3.30907408 
     280     0.02800000 -1888.67006705 -1893.88587245   158.24010430    -0.00955849     3.30955849 
     290     0.02900000 -1888.67013001 -1894.02402688   162.42960290    -0.01005424     3.31005424 
     300     0.03000000 -1888.67012741 -1893.91715254   159.18726627    -0.01056129     3.31056129 
     310     0.03100000 -1888.67005750 -1893.57037262   148.66857854    -0.01107957     3.31107957 
     320     0.03200000 -1888.66994592 -1893.09358639   134.20694885    -0.01160898     3.31160898 
     330     0.03300000 -1888.66983608 -1892.66132683   121.09614209    -0.01214935     3.31214935 
     340     0.03400000 -1888.66977429 -1892.44446364   114.51869677    -0.01270046     3.31270046 
     350     0.03500000 -1888.66978845 -1892.53901254   117.38674604    -0.01326207     3.31326207 
     360     0.03600000 -1888.66987459 -1892.92337308   129.04508370    -0.01383390     3.31383390 
     370     0.03700000 -1888.66999819 -1893.46445589   145.45701553    -0.01441561     3.31441561 
     380     0.03800000 -1888.67010979 -1893.97065536   160.81100019    -0.01500688     3.31500688 
     390     0.03900000 -1888.67016559 -1894.26835837   169.84119248    -0.01560734     3.31560734 
     400     0.04000000 -1888.67014686 -1894.26967995   169.88185548    -0.01621664     3.31621664 
     410     0.04100000 -1888.67006186 -1894.00321089   161.80014284    -0.01683442     3.31683442 
     420     0.04200000 -1888.66994386 -1893.60086344   149.59707422    -0.01746033     3.31746033 
     430     0.04300000 -1888.66984078 -1893.24559860   138.82197278    -0.01809405     3.31809405 
     440     0.04400000 -1888.66979419 -1893.09727893   134.32357877    -0.01873527     3.31873527 
     450     0.04500000 -1888.66982159 -1893.22837461   138.30000376    -0.01938373     3.31938373 
     460     0.04600000 -1888.66990991 -1893.59670402   149.47191350    -0.02003918     3.32003918 
     470     0.04700000 -1888.67002193 -1894.06542618   163.68887740    -0.02070143     3.32070143 
     480     0.04800000 -1888.67011408 -1894.46010861   175.66018436    -0.02137030     3.32137030 
     490     0.04900000 -1888.67015195 -1894.63688117   181.02206322    -0.02204565     3.32204565 
     500     0.05000000 -1888.67012178 -1894.53632241   177.97216884    -0.02272740     3.32272740 
     510     0.05100000 -1888.67003782 -1894.20444750   167.90610440    -0.02341547     3.32341547 
     520     0.05200000 -1888.66993171 -1893.77231086   154.79891357    -0.02410981     3.32410981 
     530     0.05300000 -1888.66984524 -1893.40525947   143.66572040    -0.02481040     3.32481040 
     540     0.05400000 -1888.66981428 -1893.23762103   138.58074854    -0.02551724     3.32551724 
     550     0.05500000 -1888.66985024 -1893.31793613   141.01630314    -0.02623032     3.32623032 
     560     0.05600000 -1888.66993756 -1893.59069032   149.28862746    -0.02694963     3.32694963 
     570     0.05700000 -1888.67003871 -1893.92089591   159.30352583    -0.02767517     3.32767517 
     580     0.05800000 -1888.67011342 -1894.15124772   166.28980520    -0.02840691     3.32840691 
     590     0.05900000 -1888.67013211 -1894.16548061   166.72104344    -0.02914478     3.32914478 
     600     0.06000000 -1888.67008732 -1893.93443338   159.71275857    -0.02988871     3.32988871 
     610     0.06100000 -1888.66999458 -1893.52841675   147.39760649    -0.03063856     3.33063856 
     620     0.06200000 -1888.66988829 -1893.09235041   134.17119966    -0.03139416     3.33139416 
     630     0.06300000 -1888.66981016 -1892.79172036   125.05288241    -0.03215531     3.33215531 
     640     0.06400000 -1888.66979281 -1892.74755409   123.71346729    -0.03292176     3.33292176 
     650     0.06500000 -1888.66984352 -1892.98665478   130.96590321    -0.03369323     3.33369323 
     660     0.06600000 -1888.66994264 -1893.42999887   144.41332385    -0.03446937     3.33446937 
     670     0.06700000 -1888.67005253 -1893.92310700   159.37018803    -0.03524986     3.33524986 
     680     0.06800000 -1888.67013328 -1894.29451600   170.63575807    -0.03603430     3.33603430 
     690     0.06900000 -1888.67015472 -1894.41878137   174.40514195    -0.03682229     3.33682229 
     700     0.07000000 -1888.67010916 -1894.26288055   169.67671536    -0.03761343     3.33761343 
     710     0.07100000 -1888.67001386 -1893.89812923   158.61357122    -0.03840729     3.33840729 
     720     0.07200000 -1888.66990397 -1893.47348765   145.73388461    -0.03920344     3.33920344 
     730     0.07300000 -1888.66982231 -1893.15984859   136.22099965    -0.04000148     3.34000148 
     740     0.07400000 -1888.66980129 -1893.08373765   133.91254030    -0.04080098     3.34080098 
     750     0.07500000 -1888.66984814 -1893.27755530   139.79127022    -0.04160156     3.34160156 
     760     0.07600000 -1888.66994235 -1893.66837384   151.64528962    -0.04240282     3.34240282 
     770     0.07700000 -1888.67004573 -1894.10941225   165.02263022    -0.04320441     3.34320441 
     780     0.07800000 -1888.67011722 -1894.43947564   175.03411433    -0.04400599     3.34400599 
     790     0.07900000 -1888.67013317 -1894.54590490   178.26254255    -0.04480726     3.34480726 
     800     0.08000000 -1888.67008771 -1894.40384162   173.95392409    -0.04560792     3.34560792 
     810     0.08100000 -1888.66999942 -1894.08389023   164.24973325    -0.04640773     3.34640773 
     820     0.08200000 -1888.66990467 -1893.72313999   153.30795968    -0.04720647     3.34720647 
     830     0.08300000 -1888.66984387 -1893.46839210   145.58111627    -0.04800393     3.34800393 
     840     0.08400000 -1888.66984175 -1893.41412556   143.93481091    -0.04879995     3.34879995 
     850     0.08500000 -1888.66989690 -1893.56426173   148.48805548    -0.04959439     3.34959439 
     860     0.08600000 -1888.66998242 -1893.83463738   156.68827289    -0.05038713     3.35038713 
     870     0.08700000 -1888.67006191 -1894.09325064   164.53181916    -0.05117805     3.35117805 
     880     0.08800000 -1888.67010292 -1894.21712680   168.28880099    -0.05196706     3.35196706 
     890     0.08900000 -1888.67009013 -1894.14263970   166.02935659    -0.05275408     3.35275408 
     900     0.09000000 -1888.67002911 -1893.89014590   158.37090593    -0.05353904     3.35353904 
     910     0.09100000 -1888.66994346 -1893.55535729   148.21649476    -0.05432186     3.35432186 
     920     0.09200000 -1888.66986545 -1893.27257968   139.63979183    -0.05510247     3.35510247 
     930     0.09300000 -1888.66982750 -1893.16330910   136.32582951    -0.05588078     3.35588078 
     940     0.09400000 -1888.66984650 -1893.28643304   140.06065783    -0.05665670     3.35665670 
     950     0.09500000 -1888.66991522 -1893.61245361   149.94957262    -0.05743015     3.35743015 
     960     0.09600000 -1888.67000710 -1894.03423941   162.74316510    -0.05820101     3.35820101 
     970     0.09700000 -1888.67008668 -1894.40848044   174.09469033    -0.05896915     3.35896915 
     980     0.09800000 -1888.67012456 -1894.61056787   180.22458605    -0.05973444     3.35973444 
     990     0.09900000 -1888.67010627 -1894.58107679   179.33042341    -0.06049672     3.36049672 
    1000     0.10000000 -1888.67004000 -1894.34773324   172.25312335    -0.06125581     3.36125581 
Loop time of 1.55992 on 4 procs for 1000 steps with 256 atoms

Performance: 5.539 ns/day, 4.333 hours/ns, 641.059 timesteps/s
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.3161     | 1.3724     | 1.4128     |   3.0 | 87.98
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.11734    | 0.16017    | 0.21617    |   8.9 | 10.27
Output  | 0.0032182  | 0.0051764  | 0.010916   |   4.6 |  0.33
Modify  | 0.0020187  | 0.0022321  | 0.0026002  |   0.5 |  0.14
Other   |            | 0.0199     |            |       |  1.28

Nlocal:    64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    1265 ave 1265 max 1265 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    9328 ave 9328 max 9328 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:  23648 ave 23648 max 23648 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 94592
Ave neighs/atom = 369.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01
